Bug Description

How to reproduce:
1. Install a JAVA application. In my case, I am running Matlab 2011a.
2. Open it.

What should happen:
Show a nicely rendered window.

What happens instead:
The window is not properly shown and cut-off at the bottom and right hand side. There are also strange artifacts and the Nautilus selection tooltip is displayed in the lower right corner. This is a regression from 11.04.

Recommended importance:
High. This bug prevents deployment of Ubuntu 11.10 to academic institutions, because widespread, high value software can not be executed properly. This includes e.g. Matlab, Maple, etc.

racarr says this is fixed in the oneiric branch with applications like CGoban from gokgs.com . Can you check if you can reproduce the bug with that application as well? If so, then I'm willing to bet that this is probably fixed somehow [tm]